LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - dimer particles

units           lj
atom_style      sphere
atom_modify     map array first big
dimension       2

# read in clusters of rigid bodies

fix             molprop all property/atom mol ghost yes
read_data       data.dimer fix molprop NULL Molecules
Reading data file ...
  orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  200 atoms
  read_data CPU = 0.001 seconds

set             type 1 mass 1.0
Setting atom values ...
  200 settings made for mass
group           big type 1
200 atoms in group big
velocity        big create 1.44 87287 loop geom

# equilibrate big particles

pair_style      soft 1.12
pair_coeff      1 1 0.0
pair_coeff      2 2 0.0 0.0
pair_coeff      1 2 0.0 0.0

variable        prefactor equal ramp(0,60)
fix             soft all adapt 1 pair soft a * * v_prefactor

fix             1 big rigid molecule
  100 rigid bodies with 200 atoms
fix             2 all enforce2d

#dump           1 all atom 10 dump.dimer.equil

thermo          100
run             1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.42
  ghost atom cutoff = 1.42
  binsize = 0.71, bins = 27 27 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair soft, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   3.4028231      0              0              0.83369167    -0.55065517   
       100   9.5167872      2.392105       0              4.7237178      2.8319556    
       200   13.564465      3.0352634      0              6.3585572      3.6388732    
       300   13.133051      4.3835112      0              7.6011086      4.060051     
       400   14.576837      5.5141059      0              9.0854309      4.422762     
       500   15.227825      6.6472106      0              10.378028      4.8598912    
       600   16.93219       7.454865       0              11.603251      5.2908894    
       700   16.573769      8.7323442      0              12.792918      5.3544684    
       800   17.482599      9.7221047      0              14.005341      5.6200973    
       900   18.548144      10.739353      0              15.283649      4.7817995    
      1000   18.068079      12.058417      0              16.485096      6.5773091    
Loop time of 0.0502552 on 1 procs for 1000 steps with 200 atoms

Performance: 8596132.389 tau/day, 19898.455 timesteps/s, 3.980 Matom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0095071  | 0.0095071  | 0.0095071  |   0.0 | 18.92
Neigh   | 0.0042809  | 0.0042809  | 0.0042809  |   0.0 |  8.52
Comm    | 0.0022049  | 0.0022049  | 0.0022049  |   0.0 |  4.39
Output  | 0.0001259  | 0.0001259  | 0.0001259  |   0.0 |  0.25
Modify  | 0.032467   | 0.032467   | 0.032467   |   0.0 | 64.60
Other   |            | 0.00167    |            |       |  3.32

Nlocal:            200 ave         200 max         200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             64 ave          64 max          64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            275 ave         275 max         275 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 275
Ave neighs/atom = 1.375
Neighbor list builds = 193
Dangerous builds = 0

#undump         1
unfix           soft
unfix           1
unfix           2

# add small particles as hi density lattice

region          plane block INF INF INF INF -0.001 0.001 units box
lattice         sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms    2 region plane
Created 29929 atoms
  using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
  create_atoms CPU = 0.006 seconds

set             type 2 mass 0.1
Setting atom values ...
  29929 settings made for mass
group           small type 2
29929 atoms in group small
velocity        small create 1.0 593849 loop geom

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.5

delete_atoms    overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 14 14 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 12776 atoms, new total = 17353

# SRD run

reset_timestep  0

neighbor        0.3 multi
neigh_modify    delay 0 every 1 check yes

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.001

fix             1 big rigid molecule
  100 rigid bodies with 200 atoms
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
fix             3 small viscosity 10 x y 50
fix             4 all enforce2d

# diagnostics

compute         tbig big temp/sphere
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)
thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]

thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo          1000

#dump           1 all atom 500 dump.dimer.mp

#dump           1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2

run             25000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 17153 200
  big particle diameter max/min = 1 1
  SRD temperature & lamda = 1 0.063245553
  SRD max distance & max velocity = 0.25298221 12.649111
  SRD grid counts: 75 75 1
  SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
  SRD per actual grid cell = 5.544404
  SRD viscosity = 0.23553122
  big/SRD mass density ratio = 0.14250828
  # of rescaled SRD velocities = 0
  ave/max small velocity = 4.191188 7.6900178
  ave/max big velocity = 2.6813242 7.1846104
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 18.683304, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
         0   6.8392143      0              0.297476       20.71529       25.810505      4.0555741      0              0              0              0              0              0              0              0              0              0              0              0            
      1000   1.3421139      3394           0.24797209     20.515424      21.515299      5.9986227      13474          52             52             1              704            16900          5625           3394           1.1328453      0              14             0            
      2000   1.3372296      3366           0.24694513     20.429958      21.426194      9.640193       13302          74             74             0              1516           16900          5625           3366           1.1634167      0              14             0            
      3000   1.4022742      3360           0.24799552     20.472637      21.517331      5.9446731      13483          47             47             0              2989           16900          5625           3360           1.1774442      0              217            0            
      4000   1.6325677      3376           0.25066282     20.532497      21.74876       6.9698781      13206          61             61             2              4198           16900          5625           3376           1.1749717      0              217            0            
      5000   2.0992887      3391           0.25484065     20.547279      22.111249      10.648531      13414          62             69             1              6389           16900          5625           3391           1.1862903      0              412            0            
      6000   1.7584548      3388           0.25126127     20.490636      21.800684      8.68036        13456          58             58             0              7672           16900          5625           3388           1.1553986      0              412            0            
      7000   2.2384486      3343           0.25650382     20.58791       22.255554      12.008146      13187          59             59             0              8879           16900          5625           3343           1.1728994      0              412            0            
      8000   2.4981644      3380           0.25734806     20.467672      22.328804      6.7156077      13383          51             51             0              10085          16900          5625           3380           1.156205       0              412            0            
      9000   2.4321991      3384           0.25838085     20.606426      22.418415      9.9820399      12847          55             55             0              11445          16900          5625           3384           1.156145       0              412            0            
     10000   2.2560205      3387           0.25541566     20.480404      22.161139      10.87418       13022          66             66             0              12863          16900          5625           3387           1.1559136      0              412            0            
     11000   2.2321955      3378           0.25533735     20.491359      22.154345      8.510825       13175          70             70             1              14273          16900          5625           3378           1.1470284      0              412            0            
     12000   2.2715125      3377           0.25469529     20.40636       22.098637      9.0604601      13146          68             68             0              15742          16900          5625           3377           1.171755       0              412            0            
     13000   2.3766974      3364           0.25667348     20.499635      22.270275      10.766786      12829          60             60             1              17214          16900          5625           3364           1.130354       0              412            0            
     14000   2.5659704      3347           0.25802994     20.47632       22.387967      8.2568074      13090          66             66             1              18767          16900          5625           3347           1.1609852      0              412            0            
     15000   2.3235671      3400           0.25603152     20.483517      22.214574      5.4785711      13389          50             50             0              20173          16900          5625           3400           1.149754       0              412            0            
     16000   2.6335413      3373           0.25956137     20.558854      22.520843      4.7121947      13027          58             58             1              21668          16900          5625           3373           1.1308267      0              412            0            
     17000   2.5603168      3410           0.25744829     20.430065      22.337501      6.1898616      13218          51             51             1              23170          16900          5625           3410           1.1285699      0              412            0            
     18000   2.7801428      3362           0.26002524     20.489884      22.56109       8.9919312      13002          57             57             3              24829          16900          5625           3362           1.1610153      0              412            0            
     19000   2.7869738      3364           0.26033026     20.51126       22.587555      9.6539159      13085          46             46             0              26476          16900          5625           3364           1.1431913      0              412            0            
     20000   2.678182       3383           0.2586317      20.444934      22.44018       7.3468277      12939          42             42             0              27992          16900          5625           3383           1.143534       0              412            0            
     21000   2.8094503      3375           0.26088069     20.542272      22.635313      8.2257869      13449          52             52             0              29570          16900          5625           3375           1.1375499      0              412            0            
     22000   3.2220363      3377           0.26464914     20.561866      22.962283      6.6329375      13178          65             65             6              31203          16900          5625           3377           1.1683184      0              412            0            
     23000   3.2268368      3339           0.26414495     20.514543      22.918536      4.6879815      12589          51             51             0              32929          16900          5625           3339           1.1378613      0              412            0            
     24000   2.6062461      3380           0.25967238     20.588821      22.530474      10.036449      12745          53             54             0              34460          16900          5625           3380           1.1396017      0              412            0            
     25000   3.2519674      3373           0.26376614     20.462953      22.885669      7.7592712      12856          52             52             1              36172          16900          5625           3373           1.1858891      0              412            0            
Loop time of 20.7208 on 1 procs for 25000 steps with 17353 atoms

Performance: 104243.242 tau/day, 1206.519 timesteps/s, 20.937 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.39343    | 0.39343    | 0.39343    |   0.0 |  1.90
Neigh   | 0.09039    | 0.09039    | 0.09039    |   0.0 |  0.44
Comm    | 0.26483    | 0.26483    | 0.26483    |   0.0 |  1.28
Output  | 0.0021023  | 0.0021023  | 0.0021023  |   0.0 |  0.01
Modify  | 19.785     | 19.785     | 19.785     |   0.0 | 95.49
Other   |            | 0.1847     |            |       |  0.89

Nlocal:          17353 ave       17353 max       17353 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            146 ave         146 max         146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           1326 ave        1326 max        1326 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1326
Ave neighs/atom = 0.0764133
Neighbor list builds = 1290
Dangerous builds = 0
Total wall time: 0:00:21
